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- PDB-2eh8: Crystal structure of the complex of humanized KR127 fab and PRES1... -

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Basic information

Entry
Database: PDB / ID: 2eh8
TitleCrystal structure of the complex of humanized KR127 fab and PRES1 peptide epitope
Components
  • HUMANIZED KR127 FAB, HEAVY CHAIN
  • HUMANIZED KR127 FAB, LIGHT CHAIN
  • PreS1/PreS2/surface protein
KeywordsIMMUNE SYSTEM / HEPATITIS B VIRUS / HUMANIZED ANTIBODY / MONOCLONAL ANTIBODY / NEUTRALIZATION / PRES1
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Large envelope protein S / Major surface antigen from hepadnavirus / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Large envelope protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChi, S.-W. / Kim, S.-J. / Maeng, C.-Y. / Hong, H.J. / Ryu, S.-E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Broadly neutralizing anti-hepatitis B virus antibody reveals a complementarity determining region H3 lid-opening mechanism
Authors: Chi, S.-W. / Maeng, C.-Y. / Kim, S.J. / Oh, M.S. / Ryu, C.J. / Kim, S.-J. / Han, K.-H. / Hong, H.J. / Ryu, S.-E.
History
DepositionMar 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: HUMANIZED KR127 FAB, LIGHT CHAIN
H: HUMANIZED KR127 FAB, HEAVY CHAIN
P: PreS1/PreS2/surface protein


Theoretical massNumber of molelcules
Total (without water)48,1693
Polymers48,1693
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.340, 61.270, 83.540
Angle α, β, γ (deg.)90.00, 93.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody HUMANIZED KR127 FAB, LIGHT CHAIN


Mass: 23788.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HUMANIZED KR127 / Plasmid: PCMV / Cell (production host): DHFR-DEFICIENT CHO CELL / Cell line (production host): DG44 / Production host: Homo sapiens (human)
#2: Antibody HUMANIZED KR127 FAB, HEAVY CHAIN


Mass: 23086.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HUMANIZED KR127 / Plasmid: PCMV / Cell (production host): DHFR-DEFICIENT CHO CELL / Cell line (production host): DG44 / Production host: Homo sapiens (human)
#3: Protein/peptide PreS1/PreS2/surface protein


Mass: 1293.256 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide P was chemically synthesized. The sequence is naturally found in hepatitis B virus.
References: UniProt: Q2EID8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SHORT PEPTIDE, PRES1, IS AMIDATED /ACETYLATED AT THE N- AND C-TERMINUS, RESPECTIVELY. A ...THE SHORT PEPTIDE, PRES1, IS AMIDATED /ACETYLATED AT THE N- AND C-TERMINUS, RESPECTIVELY. A SEQUENCE DATABASE REFERENCE FOR CHAIN L AND H NOT CURRENTLY EXIST. THE SEQUENCES ARE SHOWN IN THE PAPER(FIGURE 1): HONG, H.J. ET AL., VIROLOGY 318, 134-141 (2004)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 4000, 10mM Hepes-NaOH, 0.2M ammonium sulfate, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 30, 2001
RadiationMonochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→32.91 Å / Num. all: 14984 / Num. obs: 14611 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.74 Å / % possible all: 96.1

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EH7

2eh7


Resolution: 2.6→32.91 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 730 -RANDOM
Rwork0.193 ---
obs0.193 14611 97.5 %-
all-14984 --
Refinement stepCycle: LAST / Resolution: 2.6→32.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 0 41 3420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.97

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